Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

{
    "fileformat": "VCFv4.2",
    "FILTER": "<ID=PASS,Description=\"All filters passed\">",
    "INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
    "FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
    "FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
    "FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
    "FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
    "FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
    "FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
    "FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
    "META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
    "META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
    "META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
    "META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
    "META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
    "META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
    "META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
    "META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
    "SAMPLE": "<ID=ukb-d-1418_2,TotalVariants=13586586,VariantsNotRead=0,HarmonisedVariants=13586586,VariantsNotHarmonised=0,SwitchedAlleles=229,StudyType=Continuous>",
    "contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
    "contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
    "contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
    "contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
    "contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
    "contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
    "contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
    "contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
    "contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
    "contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
    "contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
    "contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
    "contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
    "contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
    "contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
    "contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
    "contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
    "contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
    "contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
    "contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
    "contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
    "contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
    "contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
    "contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
    "contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
    "contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
    "contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
    "contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
    "contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
    "contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
    "contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
    "contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
    "contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
    "contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
    "contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
    "contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
    "contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
    "contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
    "contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
    "contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
    "contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
    "contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
    "contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
    "contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
    "contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
    "contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
    "contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
    "contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
    "contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
    "contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
    "contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
    "contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
    "contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
    "contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
    "contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
    "contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
    "contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
    "contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
    "contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
    "contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
    "contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
    "contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
    "contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
    "contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
    "contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
    "contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
    "contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
    "contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
    "contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
    "contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
    "contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
    "contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
    "contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
    "contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
    "contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
    "contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
    "contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
    "contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
    "contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
    "contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
    "contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
    "contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
    "contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
    "contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1418_2/ukb-d-1418_2_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
    "file_date": "2019-11-25T15:35:15.937861",
    "bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1418_2/ukb-d-1418_2.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1418_2/ukb-d-1418_2_data.vcf.gz; Date=Mon Nov 25 16:26:15 2019",
    "bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-1418_2/ukb-d-1418_2.vcf.gz; Date=Sun May 10 23:22:00 2020"
}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1418_2/ukb-d-1418_2.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1418_2/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 17:06:16 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1418_2/ukb-d-1418_2.vcf.gz ...
Read summary statistics for 13586586 SNPs.
Dropped 12711 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0133 (0.0014)
Lambda GC: 1.0892
Mean Chi^2: 1.0967
Intercept: 1.002 (0.006)
Ratio: 0.0206 (0.0617)
Analysis finished at Mon Nov 25 17:08:34 2019
Total time elapsed: 2.0m:17.97s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0513,
    "mean_EFFECT": -0,
    "n": 360806,
    "n_snps": 13586586,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1251809,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 569292,
    "n_est": 362181.1158,
    "ratio_se_n": 1.0019,
    "mean_diff": -0,
    "ratio_diff": 161.9762,
    "sd_y_est1": 0.477,
    "sd_y_est2": 0.4779,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0133,
    "ldsc_observed_scale_h2_se": 0.0014,
    "ldsc_intercept_beta": 1.002,
    "ldsc_intercept_se": 0.006,
    "ldsc_lambda_gc": 1.0892,
    "ldsc_mean_chisq": 1.0967,
    "ldsc_ratio": 0.0207
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio FALSE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

General metrics

  • af_correlation: Correlation coefficient between AF and AF_reference.
  • inflation_factor (lambda): Genomic inflation factor.
  • mean_EFFECT: Mean of EFFECT size.
  • n: Maximum value of reported sample size across all SNPs, \(n\).
  • n_clumped_hits: Number of clumped hits.
  • n_snps: Number of SNPs
  • n_p_sig: Number of SNPs with pvalue below 5e-8.
  • n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
  • n_ns: Number of SNPs with nonsense values:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 0 or > 1.
  • n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
  • is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
  • n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

  • n_est: Estimated sample size value, \(\widehat{n}\).
  • ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
  • mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

  • r2_sum<*>: r2 statistics under various assumptions
    • 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
    • 2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),
    • 3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),
    • 4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).

LDSC metrics

Metrics from LD regression

  • ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
  • ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
  • ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
  • ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
  • ldsc_lambda_gc: Lambda GC statistics.
  • ldsc_mean_chisq: Mean \(\chi^2\) statistics.
  • ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

  • af_correlation: abs(af_correlation) < 0.7.
  • inflation_factor: inflation_factor > 1.2.
  • n: n (max reported sample size) < 10000.
  • is_snpid_non_unique: NOT is_snpid_unique.
  • mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
  • mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
  • mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
  • mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
  • n_p_sig: n_p_sig > 1000.
  • miss_<*>: n_miss_<*> / n_snps > 0.01.
  • ldsc_ratio: ldsc_ratio > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.000000 3 94 0 13574539 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 100 0 57083 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 342 0 33337 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.051332e+00 6.184961e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.902504e+07 5.591474e+07 3.02000e+02 3.293101e+07 7.013846e+07 1.148589e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA -1.500000e-05 6.573300e-03 -8.89907e-02 -1.797700e-03 -1.350000e-05 1.776100e-03 7.816640e-02 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 4.718500e-03 4.551600e-03 9.23300e-04 1.343300e-03 2.475500e-03 6.781000e-03 2.289370e-02 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.916849e-01 2.911148e-01 1.00000e-07 2.373788e-01 4.892006e-01 7.437175e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.916845e-01 2.911151e-01 1.00000e-07 2.373777e-01 4.892006e-01 7.437167e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA 1.908017e-01 2.544021e-01 1.00000e-03 7.429400e-03 6.003010e-02 2.953020e-01 9.989990e-01 ▇▂▁▁▁
numeric AF_reference 569292 0.958099 NA NA NA NA NA 1.963330e-01 2.471006e-01 0.00000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.000000 NA NA NA NA NA 3.608060e+05 0.000000e+00 3.60806e+05 3.608060e+05 3.608060e+05 3.608060e+05 3.608060e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0021778 0.0019664 0.2680730 0.2680730 0.1106400 0.1894970 360806
1 693731 rs12238997 A G 0.0029511 0.0018579 0.1122000 0.1121982 0.1158360 0.1417730 360806
1 707522 rs371890604 G C 0.0042127 0.0020888 0.0437109 0.0437100 0.0973005 0.1293930 360806
1 717587 rs144155419 G A 0.0014012 0.0049838 0.7785885 0.7785887 0.0156910 0.0045926 360806
1 723329 rs189787166 A T 0.0306940 0.0147044 0.0368519 0.0368518 0.0017340 0.0003994 360806
1 730087 rs148120343 T C 0.0048254 0.0025885 0.0622974 0.0622965 0.0564560 0.0127796 360806
1 731718 rs142557973 T C 0.0026608 0.0017620 0.1310340 0.1310341 0.1217420 0.1543530 360806
1 732032 rs61770163 A C 0.0026876 0.0018796 0.1527429 0.1527414 0.1211750 0.1555510 360806
1 734349 rs141242758 T C 0.0028651 0.0017630 0.1041300 0.1041305 0.1209690 0.1525560 360806
1 740284 rs61770167 C T 0.0031399 0.0080658 0.6970646 0.6970636 0.0057852 0.0023962 360806
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0045462 0.0020360 0.0255517 0.0255508 0.0561637 0.0309934 360806
23 154923374 rs111332691 T A 0.0030126 0.0022374 0.1781550 0.1781537 0.0447817 0.0116556 360806
23 154925045 rs509981 C T -0.0009236 0.0010765 0.3909372 0.3909346 0.2456180 0.3634440 360806
23 154925895 rs538470 C T -0.0008484 0.0011012 0.4410776 0.4410755 0.2419280 0.3634440 360806
23 154927581 rs644138 G A 0.0003555 0.0010124 0.7254843 0.7254842 0.3021690 0.4635760 360806
23 154929412 rs557132 C T -0.0009362 0.0010768 0.3846210 0.3846206 0.2454700 0.3568210 360806
23 154929637 rs35185538 CT C -0.0010148 0.0011238 0.3665540 0.3665526 0.2297070 0.3011920 360806
23 154929952 rs4012982 CAA C -0.0008105 0.0011326 0.4742027 0.4742018 0.2394320 0.3165560 360806
23 154930230 rs781880 A G -0.0007959 0.0010767 0.4597640 0.4597619 0.2458800 0.3618540 360806
23 154930487 rs781879 T A 0.0018094 0.0036931 0.6241745 0.6241740 0.0195658 0.1263580 360806

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11064  ES:SE:LP:AF:SS:ID   0.00217781:0.0019664:0.571747:0.11064:360806:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115836 ES:SE:LP:AF:SS:ID   0.00295107:0.0018579:0.950007:0.115836:360806:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0973005    ES:SE:LP:AF:SS:ID   0.00421274:0.00208876:1.35941:0.0973005:360806:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015691 ES:SE:LP:AF:SS:ID   0.00140123:0.00498377:0.108692:0.015691:360806:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00173396   ES:SE:LP:AF:SS:ID   0.030694:0.0147044:1.43354:0.00173396:360806:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056456 ES:SE:LP:AF:SS:ID   0.00482541:0.00258849:1.20553:0.056456:360806:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121742 ES:SE:LP:AF:SS:ID   0.00266076:0.00176205:0.882616:0.121742:360806:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121175 ES:SE:LP:AF:SS:ID   0.00268764:0.00187958:0.816039:0.121175:360806:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120969 ES:SE:LP:AF:SS:ID   0.00286514:0.001763:0.982424:0.120969:360806:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00578523   ES:SE:LP:AF:SS:ID   0.00313991:0.00806579:0.156727:0.00578523:360806:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00187907   ES:SE:LP:AF:SS:ID   -0.0176955:0.0152264:0.610529:0.00187907:360806:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869735 ES:SE:LP:AF:SS:ID   -0.00195005:0.00173804:0.581914:0.869735:360806:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00152775   ES:SE:LP:AF:SS:ID   0.0121589:0.015751:0.3564:0.00152775:360806:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.122925 ES:SE:LP:AF:SS:ID   0.00201301:0.00172129:0.615801:0.122925:360806:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14272  ES:SE:LP:AF:SS:ID   0.00144226:0.00170137:0.401644:0.14272:360806:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123041 ES:SE:LP:AF:SS:ID   0.00200765:0.0017189:0.614728:0.123041:360806:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87088  ES:SE:LP:AF:SS:ID   -0.0019462:0.00167502:0.610343:0.87088:360806:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875464 ES:SE:LP:AF:SS:ID   -0.0019742:0.00170279:0.608541:0.875464:360806:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128641 ES:SE:LP:AF:SS:ID   0.00197128:0.0016792:0.619033:0.128641:360806:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.03637  ES:SE:LP:AF:SS:ID   -0.00617881:0.00304622:1.37136:0.03637:360806:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870473 ES:SE:LP:AF:SS:ID   -0.00201874:0.00167328:0.642748:0.870473:360806:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870579 ES:SE:LP:AF:SS:ID   -0.002055:0.00167404:0.658348:0.870579:360806:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87047  ES:SE:LP:AF:SS:ID   -0.00202618:0.00167321:0.646055:0.87047:360806:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00504757   ES:SE:LP:AF:SS:ID   -0.0032124:0.00858686:0.149767:0.00504757:360806:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00501451   ES:SE:LP:AF:SS:ID   -0.00341919:0.00860984:0.160349:0.00501451:360806:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558365   ES:SE:LP:AF:SS:ID   -0.00759768:0.00832153:0.44221:0.00558365:360806:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870553 ES:SE:LP:AF:SS:ID   -0.00189219:0.00167027:0.589611:0.870553:360806:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125995 ES:SE:LP:AF:SS:ID   0.00214436:0.00170427:0.681286:0.125995:360806:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870116 ES:SE:LP:AF:SS:ID   -0.00187495:0.00166624:0.584221:0.870116:360806:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869403 ES:SE:LP:AF:SS:ID   -0.00193071:0.00166472:0.608816:0.869403:360806:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87027  ES:SE:LP:AF:SS:ID   -0.00187608:0.00166768:0.584016:0.87027:360806:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870276 ES:SE:LP:AF:SS:ID   -0.00187747:0.0016678:0.584551:0.870276:360806:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870285 ES:SE:LP:AF:SS:ID   -0.00188733:0.00166785:0.588705:0.870285:360806:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870728 ES:SE:LP:AF:SS:ID   -0.0018886:0.0016721:0.58721:0.870728:360806:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0988444    ES:SE:LP:AF:SS:ID   0.00322713:0.00194314:1.01432:0.0988444:360806:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00647302   ES:SE:LP:AF:SS:ID   -0.00691582:0.00751772:0.446594:0.00647302:360806:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874626 ES:SE:LP:AF:SS:ID   -0.00200444:0.00169703:0.624252:0.874626:360806:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864015 ES:SE:LP:AF:SS:ID   -0.00151214:0.00166418:0.439448:0.864015:360806:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869416 ES:SE:LP:AF:SS:ID   -0.00194808:0.00168034:0.608502:0.869416:360806:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86636  ES:SE:LP:AF:SS:ID   -0.00210239:0.00168068:0.67579:0.86636:360806:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0987861    ES:SE:LP:AF:SS:ID   0.00253894:0.00201213:0.683996:0.0987861:360806:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871547 ES:SE:LP:AF:SS:ID   -0.00221595:0.00169984:0.715883:0.871547:360806:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871547 ES:SE:LP:AF:SS:ID   -0.00221642:0.00169984:0.716095:0.871547:360806:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871546 ES:SE:LP:AF:SS:ID   -0.00222378:0.00169987:0.719415:0.871546:360806:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87192  ES:SE:LP:AF:SS:ID   -0.00225799:0.00170084:0.73443:0.87192:360806:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125571 ES:SE:LP:AF:SS:ID   0.00198134:0.00170216:0.611863:0.125571:360806:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105431 ES:SE:LP:AF:SS:ID   0.00306892:0.00185309:1.01011:0.105431:360806:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855365 ES:SE:LP:AF:SS:ID   -0.00218607:0.00166354:0.72397:0.855365:360806:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00165469   ES:SE:LP:AF:SS:ID   0.0292791:0.014736:1.32851:0.00165469:360806:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838366 ES:SE:LP:AF:SS:ID   -0.00037999:0.00163901:0.0879582:0.838366:360806:rs376645387